Preheat the oven to 350 degrees F. Line a regular cupcake pan with 12 cupcake liners.
Sift the flour, baking powder and baking soda into a small bowl.
Add the pudding mix, wheat germ, pepper and salt to the flour mixture and set the bowl aside.
In a bowl of an electric stand mixer with a paddle attachment, cream the sugar and shortening together, until the mixture is fluffy, about 5 minutes. Scrape down the bowl and then slowly add the eggs, one egg at a time, scraping the sides of the bowl after each addition.
Add the vanilla extract.
While adding the eggs, put 2 3/4 cups water in a saucepan and bring to a boil.
Remove from the heat once the water boils.
Put the cocoa powder in a medium bowl and pour the boiling water over, whisking until smooth.
Turn off the mixer and add the liquid cocoa to the batter.
Let the mixture come together then add the dry ingredients to the batter.
Remove the bowl from the electric mixer and scrape the bowl to incorporate all the ingredients. Fold in the chopped dark chocolate.
Fill the prepared liners three-quarters full with batter and bake until a toothpick comes out clean, 18 to 20 minutes.
Let the cupcakes cool completely.
To assemble: Fill the center of the cupcakes with the Cherry Filling and top with the Pistachio Mascarpone Frosting.
Mix the cherries and cognac together in a bowl and let sit for 10 to 15 minutes.
Cream the cheese with the compound and extract (don't over mix).
